scholarly journals Refinements on electron diffraction data of β-glycine in MoPro: a quest for an improved structure model

2021 ◽  
Vol 54 (4) ◽  
Author(s):  
Kunal Kumar Jha ◽  
Barbara Gruza ◽  
Michał Leszek Chodkiewicz ◽  
Christian Jelsch ◽  
Paulina Maria Dominiak
Keyword(s):  
Electron Diffraction ◽  
Diffraction Data ◽  
Structure Determination ◽  
Structure Refinement ◽  
Electron Diffraction Data ◽  
Bethe Equation ◽  
X Ray Diffraction ◽  
X Ray ◽  
Atom Model ◽  
X Ray Scattering

The advancement in 3D electron diffraction (3D ED) techniques that lead to a revolution in molecular structure determination using nano-sized crystals is now achieving atomic resolution. The structures can be obtained from 3D ED data with tools similar to those used for X-ray structure determination. In this context, the MoPro software, originally designed for structure and charge density refinements using X-ray diffraction data, has been adapted. Structure refinement on 3D ED data was achieved via implementation of electron scattering factors available in the literature and by application of the Mott–Bethe equation to X-ray scattering factors computed from the multipolar atom model. The multipolar model was parametrized using the transferable pseudoatom databanks ELMAM2 and UBDB. Applying the independent atom model (IAM), i.e. spherical neutral atom refinement, to 3D ED data on β-glycine in MoPro resulted in structure and refinement statistics comparable to those obtained from other well known software. Use of the transferred aspherical atom model (TAAM) led to improvement of the refinement statistics and a better fit of the model to the 3D ED data as compared with the spherical atom refinement. The anisotropic displacement parameters of non-H atoms appear underestimated by typically 0.003 Å2 for the non-H atoms in IAM refinement compared with TAAM. Thus, MoPro is shown to be an effective tool for crystal structure refinement on 3D ED data and allows use of a spherical or a multipolar atom model. Electron density databases can be readily transferred with no further modification needed when the Mott–Bethe equation is applied.

A complex pseudo-decagonal quasicrystal approximant, Al37(Co,Ni)15.5, solved by rotation electron diffraction

2014 ◽  
Vol 47 (1) ◽  
pp. 215-221 ◽  
Author(s):  
Devinder Singh ◽  
Yifeng Yun ◽  
Wei Wan ◽  
Benjamin Grushko ◽  
Xiaodong Zou ◽  
...  
Keyword(s):  
Electron Diffraction ◽  
Single Crystal ◽  
Diffraction Data ◽  
Three Dimensional ◽  
Basic Structure ◽  
Electron Diffraction Data ◽  
Dimensional Electron ◽  
X Ray Diffraction ◽  
X Ray ◽  
Diffraction Patterns

Electron diffraction is a complementary technique to single-crystal X-ray diffraction and powder X-ray diffraction for structure solution of unknown crystals. Crystals too small to be studied by single-crystal X-ray diffraction or too complex to be solved by powder X-ray diffraction can be studied by electron diffraction. The main drawbacks of electron diffraction have been the difficulties in collecting complete three-dimensional electron diffraction data by conventional electron diffraction methods and the very time-consuming data collection. In addition, the intensities of electron diffraction suffer from dynamical scattering. Recently, a new electron diffraction method, rotation electron diffraction (RED), was developed, which can overcome the drawbacks and reduce dynamical effects. A complete three-dimensional electron diffraction data set can be collected from a sub-micrometre-sized single crystal in less than 2 h. Here the RED method is applied forab initiostructure determination of an unknown complex intermetallic phase, the pseudo-decagonal (PD) quasicrystal approximant Al37.0(Co,Ni)15.5, denoted as PD2. RED shows that the crystal is F-centered, witha= 46.4,b= 64.6,c= 8.2 Å. However, as with other approximants in the PD series, the reflections with oddlindices are much weaker than those withleven, so it was decided to first solve the PD2 structure in the smaller, primitive unit cell. The basic structure of PD2 with unit-cell parametersa= 23.2,b= 32.3,c= 4.1 Å and space groupPnmmhas been solved in the present study. The structure withc= 8.2 Å will be taken up in the near future. The basic structure contains 55 unique atoms (17 Co/Ni and 38 Al) and is one of the most complex structures solved by electron diffraction. PD2 is built of characteristic 2 nm wheel clusters with fivefold rotational symmetry, which agrees with results from high-resolution electron microscopy images. Simulated electron diffraction patterns for the structure model are in good agreement with the experimental electron diffraction patterns obtained by RED.

scholarly journals MicroED: a versatile cryoEM method for structure determination

2018 ◽  
Vol 2 (1) ◽  
pp. 1-8 ◽  
Author(s):  
Brent L. Nannenga ◽  
Tamir Gonen
Keyword(s):  
Electron Microscope ◽  
High Resolution ◽  
Electron Diffraction ◽  
Structure Determination ◽  
Materials Science ◽  
Electron Diffraction Data ◽  
Determination Method ◽  
X Ray Diffraction ◽  
X Ray ◽  
Transmission Electron

Micro-electron diffraction, or MicroED, is a structure determination method that uses a cryo-transmission electron microscope to collect electron diffraction data from nanocrystals. This technique has been successfully used to determine the high-resolution structures of many targets from crystals orders of magnitude smaller than what is needed for X-ray diffraction experiments. In this review, we will describe the MicroED method and recent structures that have been determined. Additionally, applications of electron diffraction to the fields of small molecule crystallography and materials science will be discussed.

On the quality of the continuous rotation electron diffraction data for accurate atomic structure determination of inorganic compounds

2018 ◽  
Vol 51 (4) ◽  
pp. 1094-1101 ◽  
Author(s):  
Yunchen Wang ◽  
Taimin Yang ◽  
Hongyi Xu ◽  
Xiaodong Zou ◽  
Wei Wan
Keyword(s):  
Electron Diffraction ◽  
Single Crystal ◽  
Diffraction Data ◽  
Structural Models ◽  
Electron Diffraction Data ◽  
Data Sets ◽  
X Ray Diffraction ◽  
X Ray ◽  
Continuous Rotation

The continuous rotation electron diffraction (cRED) method has the capability of providing fast three-dimensional electron diffraction data collection on existing and future transmission electron microscopes; unknown structures could be potentially solved and refined using cRED data collected from nano- and submicrometre-sized crystals. However, structure refinements of cRED data using SHELXL often lead to relatively high R1 values when compared with those refined against single-crystal X-ray diffraction data. It is therefore necessary to analyse the quality of the structural models refined against cRED data. In this work, multiple cRED data sets collected from different crystals of an oxofluoride (FeSeO3F) and a zeolite (ZSM-5) with known structures are used to assess the data consistency and quality and, more importantly, the accuracy of the structural models refined against these data sets. An evaluation of the precision and consistency of the cRED data by examination of the statistics obtained from the data processing software DIALS is presented. It is shown that, despite the high R1 values caused by dynamical scattering and other factors, the refined atomic positions obtained from the cRED data collected for different crystals are consistent with those of the reference models refined against single-crystal X-ray diffraction data. The results serve as a reference for the quality of the cRED data and the achievable accuracy of the structural parameters.

TAAM: a reliable and user friendly tool for hydrogen-atom location using routine X-ray diffraction data

2020 ◽  
Vol 76 (3) ◽  
pp. 296-306 ◽  
Author(s):  
Kunal Kumar Jha ◽  
Barbara Gruza ◽  
Prashant Kumar ◽  
Michal Leszek Chodkiewicz ◽  
Paulina Maria Dominiak
Keyword(s):  
Neutron Diffraction ◽  
Diffraction Data ◽  
Structure Refinement ◽  
X Rays ◽  
X Ray Diffraction ◽  
Hydrogen Atoms ◽  
X Ray ◽  
Bond Lengths ◽  
Atom Model ◽  
User Friendly

Hydrogen is present in almost all of the molecules in living things. It is very reactive and forms bonds with most of the elements, terminating their valences and enhancing their chemistry. X-ray diffraction is the most common method for structure determination. It depends on scattering of X-rays from electron density, which means the single electron of hydrogen is difficult to detect. Generally, neutron diffraction data are used to determine the accurate position of hydrogen atoms. However, the requirement for good quality single crystals, costly maintenance and the limited number of neutron diffraction facilities means that these kind of results are rarely available. Here it is shown that the use of Transferable Aspherical Atom Model (TAAM) instead of Independent Atom Model (IAM) in routine structure refinement with X-ray data is another possible solution which largely improves the precision and accuracy of X—H bond lengths and makes them comparable to averaged neutron bond lengths. TAAM, built from a pseudoatom databank, was used to determine the X—H bond lengths on 75 data sets for organic molecule crystals. TAAM parametrizations available in the modified University of Buffalo Databank (UBDB) of pseudoatoms applied through the DiSCaMB software library were used. The averaged bond lengths determined by TAAM refinements with X-ray diffraction data of atomic resolution (d min ≤ 0.83 Å) showed very good agreement with neutron data, mostly within one single sample standard deviation, much like Hirshfeld atom refinement (HAR). Atomic displacements for both hydrogen and non-hydrogen atoms obtained from the refinements systematically differed from IAM results. Overall TAAM gave better fits to experimental data of standard resolution compared to IAM. The research was accompanied with development of software aimed at providing user-friendly tools to use aspherical atom models in refinement of organic molecules at speeds comparable to routine refinements based on spherical atom model.

Applications of the maximum entropy method to powder diffraction and electron crystallography

1993 ◽  
Vol 442 (1914) ◽  
pp. 97-111 ◽  
Keyword(s):  
Electron Diffraction ◽  
Diffraction Data ◽  
Direct Methods ◽  
Entropy Method ◽  
Electron Diffraction Data ◽  
Directed Search ◽  
X Ray Diffraction ◽  
Entropy Maximization ◽  
X Ray ◽  
Trial Phase

A new multisolution phasing method based on entropy maximization and likelihood ranking, proposed for the specific purpose of increasing the accuracy and sensitivity of probabilistic phase indications compared with conventional direct methods, has been implemented and applied to a wide variety of problems. The latter comprise the determination of small crystal structures from X-ray diffraction data obtained from single crystals or from powders, and from electron diffraction data, both with and without partial phase information obtained by image processing of electron micrographs; the ranking of phase sets for a small protein; and the improvement of poor quality phases for a larger protein at medium resolution under constraint of solvent flatness. The main components of the method are (1) a tree-directed search through a space of trial phase sets; (2) the saddlepoint method for calculating joint probabilities of structure factors, using entropy maximization; (3) likelihood-based scores to rank trial phase sets and prune the search tree; (4) a statistical analysis of the scores for automatically selecting reliable phase indications. Their use is illustrated here on structure determinations from powder X-ray diffraction data and from electron diffraction data.

scholarly journals Resolution of a modulated structure by electron and powder X-ray diffraction

2014 ◽  
Vol 70 (a1) ◽  
pp. C928-C928
Author(s):  
Christophe Lepoittevin ◽  
Olivier Leynaud
Keyword(s):  
Electron Diffraction ◽  
Structure Determination ◽  
Structural Model ◽  
Zone Axis ◽  
Reciprocal Space ◽  
Electron Diffraction Data ◽  
X Ray Diffraction ◽  
Precession Angle ◽  
X Ray ◽  
Cell Parameters

These past few years, many new structures have been solved using electron diffraction methods: zone axis precession electron diffraction (PED) and tomography in reciprocal space. Both methods enable to reduce importantly the multiple scattering, so that the reflection intensities can be used for structure determination by direct methods. The ferrite Sr25Fe30O77 belongs to a family of phases whose structures consist of an intergrowth of m perovskite layers with complex rocksalt type layers [1,2]. The compound of interest is the member m = 4 of this family and its structure has been solved by combining both electron diffraction methods cited above. This oxide crystallizes in an orthorhombic system with the sub-cell parameters a ≍ b ≍ 5.4 Å and c ≍ 42 Å in a F type lattice. The structure exhibits modulation along a axis with a modulation vector q = 2/5 a. The commensurate nature of the modulation enables to describe the structure in a supercell with the cell parameters a ≍ 27 Å, b ≍ 5.4 Å and c ≍ 42 Å. PED patterns were recorded in zone axis with a Spinning Star unit using a precession angle of 20. The intensities were extracted with CRISP software and the resulting dataset was then implemented in SIR2008 for structure solution. The tomography data collection, recorded by tilting manually every 0.5 degree from -30 to +30 degrees, was inserted in a "3D Electron Diffraction Tomography" software, which reconstructs the 3D reciprocal space and extracts automatically the reflection intensities. The intensity file was then used on SIR2008 for structure determination. In order to confirm and refine the structural model, a powder X-ray diffraction pattern was performed on a laboratory diffractometer with Cu Ka1 radiation. Cell parameters were refined with the WinPlotr and FullProf Softwares using both LeBail and Rietveld methods [3]. The structural model obtained with electron diffraction data was tried and confirmed as the correct structure by the Rietveld refinements.

scholarly journals Refinement of organic crystal structures with multipolar electron scattering factors

2020 ◽  
Vol 76 (1) ◽  
pp. 92-109 ◽  
Author(s):  
Barbara Gruza ◽  
Michał Leszek Chodkiewicz ◽  
Joanna Krzeszczakowska ◽  
Paulina Maria Dominiak
Keyword(s):  
Electron Diffraction ◽  
Diffraction Data ◽  
Model Fitting ◽  
Molecular Structures ◽  
Electron Diffraction Data ◽  
X Ray Diffraction ◽  
Atom Model ◽  
Mechanical Methods ◽  
Atomic Scattering ◽  
The University

A revolution in resolution is occurring now in electron microscopy arising from the development of methods for imaging single particles at cryogenic temperatures and obtaining electron diffraction data from nanocrystals of small organic molecules or macromolecules. Near-atomic or even atomic resolution of molecular structures can be achieved. The basis of these methods is the scattering of an electron beam due to the electrostatic potential of the sample. To analyse these high-quality experimental data, it is necessary to use appropriate atomic scattering factors. The independent atom model (IAM) is commonly used although various more advanced models, already known from X-ray diffraction, can also be applied to enhance the analysis. In this study a comparison is presented of IAM and TAAM (transferable aspherical atom model), the latter with the parameters of the Hansen–Coppens multipole model transferred from the University at Buffalo Databank (UBDB). By this method, TAAM takes into account the fact that atoms in molecules are partially charged and are not spherical. Structure refinements were performed on a carbamazepine crystal using electron structure-factor amplitudes determined experimentally [Jones et al. (2018). ACS Cent. Sci. 4, 1587–1592] or modelled with theoretical quantum-mechanical methods. The results show the possibilities and limitations of the TAAM method when applied to electron diffraction. Among others, the method clearly improves model fitting statistics, when compared with IAM, and allows for reliable refinement of atomic thermal parameters. The improvements are more pronounced with poorer-resolution diffraction data.

Crystal structure analysis of a star-shaped triazine compound: a combination of single-crystal three-dimensional electron diffraction and powder X-ray diffraction

2018 ◽  
Vol 74 (3) ◽  
pp. 287-294 ◽  
Author(s):  
Tatiana E. Gorelik ◽  
Jacco van de Streek ◽  
Herbert Meier ◽  
Lars Andernach ◽  
Till Opatz
Keyword(s):  
Crystal Structure ◽  
Electron Diffraction ◽  
Single Crystal ◽  
Diffraction Data ◽  
Three Dimensional ◽  
Electron Diffraction Data ◽  
Dimensional Electron ◽  
X Ray Diffraction ◽  
Diffraction Profile ◽  
X Ray

The solid-state structure of star-shaped 2,4,6-tris{(E)-2-[4-(dimethylamino)-phenyl]ethenyl}-1,3,5-triazine is determined from a powder sample by exploiting the respective strengths of single-crystal three-dimensional electron diffraction and powder X-ray diffraction data. The unit-cell parameters were determined from single crystal electron diffraction data. Using this information, the powder X-ray diffraction data were indexed, and the crystal structure was determined from the powder diffraction profile. The compound crystallizes in a noncentrosymmetric space group,P212121. The molecular conformation in the crystal structure was used to calculate the molecular dipole moment of 3.22 Debye, which enables the material to show nonlinear optical effects.

Crystal Structure Determination of Glycerol-Containing Lipids from Electron Diffraction Data. Use of Analog Compounds Based upon Configurational Isomers of Cyclopentane-1, 2, 3-TRIOL

1977 ◽  
Vol 35 ◽  
pp. 24-25
Author(s):  
Douglas L. Dorset ◽  
Anthony J. Hancock
Keyword(s):  
Crystal Structure ◽  
Electron Diffraction ◽  
Diffraction Data ◽  
Structure Determination ◽  
Crystal Surface ◽  
Coherent Scattering ◽  
Crystal Structure Determination ◽  
Electron Diffraction Data ◽  
Polar Group ◽  
Axis Orientation

Lipids containing long polymethylene chains were among the first compounds subjected to electron diffraction structure analysis. It was only recently realized, however, that various distortions of thin lipid microcrystal plates, e.g. bends, polar group and methyl end plane disorders, etc. (1-3), restrict coherent scattering to the methylene subcell alone, particularly if undistorted molecular layers have well-defined end planes. Thus, ab initio crystal structure determination on a given single uncharacterized natural lipid using electron diffraction data can only hope to identify the subcell packing and the chain axis orientation with respect to the crystal surface. In lipids based on glycerol, for example, conformations of long chains and polar groups about the C-C bonds of this moiety still would remain unknown.One possible means of surmounting this difficulty is to investigate structural analogs of the material of interest in conjunction with the natural compound itself. Suitable analogs to the glycerol lipids are compounds based on the three configurational isomers of cyclopentane-1,2,3-triol shown in Fig. 1, in which three rotameric forms of the natural glycerol derivatives are fixed by the ring structure (4-7).

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